Im working on my centaurs and i go to use the sneak animation....as I put my animation into the game i suddenly find that all of the sneak animations (expect for idle and movement animations) have the human part rotated about 45 degree to the right (which looks weird and makes combat impossible).

I opened up the animations (the vanilla unchanged ones) in nifskope and low and behold, all these animation giving me trouble have this strange rotation on the NonAccum bone. The even stranger part is that if i load in another sneak animation that doesnt have the problem (like an idle) then the rotation will dissapear from nifskope after it runs.

Any idea on why this is?

Could you explain this in a little more detail? Sneak animations ARE rotated to the right.
First I thought this is this Blender 90° degree problem. But you are not creating own animations, are you?

I found what it was causing the weird rotation in nifskope, on some of the animation it had single animation without the NiTransformData on the NonAccum bone (which Nifskope doesnt read), and on the othder it had the NiTransformData which meant nifskope could read it and apply the proper turn.